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README.md

README.md

GenCoNet

Under development

Pipeline

  1. Prerequisites
    • Most data downloads are automatic. However some databases like DrugBank need to be downloaded manually due to licensing or the need to register an account
      • Download DrugBank full release to data/DrugBank/drugbank_all_full_database.xml.zip and extract full database.xml
      • Execute the DrugCentral queries and save them to the respective files
      • Download OMIM genemap2.txt to data/OMIM/genemap2.txt
    • Configure data/config.json to your Neo4j installation (bin path including admin tools)
  2. Execution
    1. Pre-processing
      • Run mondo.py
      • Run drugbank.py
      • Run drugcentral.py
      • Run disgenet.py
      • Run gwas_catalog.py
      • Run hgnc.py
      • Run hpo.py (WIP)
      • Run med_rt.py (WIP)
      • Run omim.py
      • Run pubmed.py
    2. Fusion
      • Run fusion.py
    3. Import database into Neo4j or directly use [output-path]/graph.json